Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF LIGAB
 
Authors :  K. Sugimoto, T. Senda, M. Fukuda, Y. Mitsui
Date :  06 Aug 98  (Deposition) - 04 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Extradiol Type Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sugimoto, T. Senda, H. Aoshima, E. Masai, M. Fukuda, Y. Mitsui
Crystal Structure Of An Aromatic Ring Opening Dioxygenase Ligab, A Protocatechuate 4, 5-Dioxygenase, Under Aerobic Conditions.
Structure V. 7 953 1999
PubMed-ID: 10467151  |  Reference-DOI: 10.1016/S0969-2126(99)80122-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4,5-DIOXYGENASE ALPHA CHAIN
    Chains: A, C
    EC Number: 1.13.11.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: SYK6
    Synonym: LIGA
 
Molecule 2 - 4,5-DIOXYGENASE BETA CHAIN
    Chains: B, D
    EC Number: 1.13.11.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: SYK6
    Synonym: LIGB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:12 , ASN B:59 , HIS B:61 , GLU B:242 , HOH B:565BINDING SITE FOR RESIDUE FE B 501
2AC2SOFTWAREHIS D:12 , ASN D:59 , HIS D:61 , GLU D:242 , HOH D:551BINDING SITE FOR RESIDUE FE D 502
3FEAUNKNOWNHIS B:12 , HIS B:61 , GLU B:242ACTIVE SITE
4FEBUNKNOWNHIS D:12 , HIS D:61 , GLU D:242ACTIVE SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BOU)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr B:157 -Pro B:158
2Gly B:192 -Met B:193
3Ile B:266 -Pro B:267
4Glu B:289 -Pro B:290
5Tyr D:157 -Pro D:158
6Gly D:192 -Met D:193
7Ile D:266 -Pro D:267
8Glu D:289 -Pro D:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BOU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BOU)

(-) Exons   (0, 0)

(no "Exon" information available for 1BOU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:132
 aligned with PCYA_SPHPI | P22635 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           PCYA_SPHPI     8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
               SCOP domains d1boua_ A: LigA subunit of an aromatic-ring-opening dioxygenase LigAB                                                                SCOP domains
               CATH domains 1bouA00 A:8-139 Protocatechuate 4,5-dioxygenase; Chain A                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh........hhhhhh.hhhhhhhhhhh.hhhhhhhhh.hhhhhhhh...hhhhhhhhh..hhhhhh....hhhhhhhhhh....hhhhhhhh....hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bou A   8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with PCYB_SPHPI | P22636 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
           PCYB_SPHPI     2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
               SCOP domains d1boub_ B: LigB subunit of an aromatic-ring-opening dioxygenase LigAB                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1bouB00 B:2-299 Protocatechuate 4,5-dioxygenase; Chain B                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhh.........hhhhhhhhhhhhhhh.......eeeeee...............eee.......................hhhhhhhhhhhhh.....eee......hhhhhhhhhhh........eeeeee..........hhhhhhhhhhhhhhhh......eeeeeee................hhhhhhhhhhhhh.hhhhhh..hhhhhhhh.hhhhhhhhhhhhhhh....eeeeeeeee.......eeeeeeee...........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bou B   2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with PCYA_SPHPI | P22635 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           PCYA_SPHPI     8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
               SCOP domains d1bouc_ C: LigA subunit of an aromatic-ring-opening dioxygenase LigAB                                                                SCOP domains
               CATH domains 1bouC00 C:8-139 Protocatechuate 4,5-dioxygenase; Chain A                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh........hhhhhh.hhhhhhhhhhh.hhhhhhhhh.hhhhhhhh...hhhhhhhh...hhhhhh....hhhhhhhhhhh...hhhhhhhh....hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bou C   8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with PCYB_SPHPI | P22636 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
           PCYB_SPHPI     2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
               SCOP domains d1boud_ D: LigB subunit of an aromatic-ring-opening dioxygenase LigAB                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1bouD00 D:2-299 Protocatechuate 4,5-dioxygenase; Chain B                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhh.........hhhhhhhhhhhhhhh.......eeeeee...............eee.......................hhhhhhhhhhhhh.....eee......hhhhhhhhhhh........eeeeee..........hhhhhhhhhhhhhhhh......eeeeeee................hhhhhhhhhhhhh.hhhhhh..hhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee.......eeeeeeeehhh........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bou D   2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BOU)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (PCYA_SPHPI | P22635)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0018579    protocatechuate 4,5-dioxygenase activity    Catalysis of the reaction: protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain B,D   (PCYB_SPHPI | P22636)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0018579    protocatechuate 4,5-dioxygenase activity    Catalysis of the reaction: protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    FEA  [ RasMol ]  +environment [ RasMol ]
    FEB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:289 - Pro B:290   [ RasMol ]  
    Glu D:289 - Pro D:290   [ RasMol ]  
    Gly B:192 - Met B:193   [ RasMol ]  
    Gly D:192 - Met D:193   [ RasMol ]  
    Ile B:266 - Pro B:267   [ RasMol ]  
    Ile D:266 - Pro D:267   [ RasMol ]  
    Tyr B:157 - Pro B:158   [ RasMol ]  
    Tyr D:157 - Pro D:158   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1bou
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PCYA_SPHPI | P22635
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PCYB_SPHPI | P22636
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.8
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PCYA_SPHPI | P22635
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PCYB_SPHPI | P22636
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCYA_SPHPI | P22635: 1b4u
        PCYB_SPHPI | P22636: 1b4u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BOU)